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相关概念视频

Electronic Structure of Atoms02:28

Electronic Structure of Atoms

20.7K

An atom comprises protons and neutrons, which are contained inside the dense, central core called the nucleus, with electrons present around the nucleus. Taking into account the wave–particle duality of electrons and the uncertainty in position around the nucleus, quantum mechanics provides a more accurate model for the atomic structure. It describes atomic orbitals as the regions around the nucleus where electrons of discrete energy exist, characterized by four quantum...
20.7K
Lewis Structures and Formal Charges02:19

Lewis Structures and Formal Charges

13.8K
Lewis symbols can be used to indicate the formation of covalent bonds, which are shown in Lewis structures—drawings that describe the bonding in molecules and polyatomic ions. The periodic table can be used to predict the number of valence electrons in an atom and the number of bonds that will be formed to reach an octet. Group 18 elements, such as argon and helium, have filled electron configurations and thus rarely participate in chemical bonding. However, atoms from group 17, such as...
13.8K
Formal Charges02:42

Formal Charges

32.1K
In some cases, there are seemingly more than one valid Lewis structures for molecules and polyatomic ions. The concept of formal charges can be used to help predict the most appropriate Lewis structure when more than one reasonable structure exists.
32.1K
The Quantum-Mechanical Model of an Atom02:45

The Quantum-Mechanical Model of an Atom

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Shortly after de Broglie published his ideas that the electron in a hydrogen atom could be better thought of as being a circular standing wave instead of a particle moving in quantized circular orbits, Erwin Schrödinger extended de Broglie’s work by deriving what is now known as the Schrödinger equation. When Schrödinger applied his equation to hydrogen-like atoms, he was able to reproduce Bohr’s expression for the energy and, thus, the Rydberg formula governing...
41.6K
Molecular Geometry and Dipole Moments02:36

Molecular Geometry and Dipole Moments

12.3K
The VSEPR theory can be used to determine the electron pair geometries and molecular structures as follows:
12.3K
VSEPR Theory02:37

VSEPR Theory

8.7K
Valence shell electron-pair repulsion theory (VSEPR theory) enables us to predict the molecular structure around a central atom from an examination of the number of bonds and lone electron pairs in its Lewis structure. The VSEPR model assumes that electron pairs in the valence shell of a central atom will adopt an arrangement that minimizes repulsions between these electron pairs by maximizing the distance between them. The electrons in the valence shell of a central atom form either bonding...
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Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid
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PDBCharges:用于PDB结构的量子力学部分原子电荷.

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  • 1CEITEC-Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic.

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计算蛋白质结构的部分原子电荷对于理解化学反应性至关重要. 新的PDBCharges网络应用程序提供了一种快速和易于使用的方法,可以从蛋白质数据库 (PDB) 结构中计算这些费用.

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科学领域:

  • 结构生物学 结构生物学
  • 计算化学计算化学
  • 生物化学 生物化学

背景情况:

  • 蛋白质数据库 (PDB) 拥有超过23万个经过实验确定的蛋白质结构.
  • 部分原子电荷对于理解来自电子密度分布的蛋白质化学反应性至关重要.
  • 对于大和可变的蛋白质结构来说,计算部分原子电荷的现有方法在准确性和通用性上是有限的.

研究的目的:

  • 介绍PDBCharges,一种用于快速计算蛋白质结构的部分原子电荷的新型网络应用程序.
  • 提供一个用户友好的工具来访问和可视化来自PDB的原子电荷数据.

主要方法:

  • 使用GFN1-xTB半经验量子力学方法进行电荷计算.
  • 保证的GFN1-xTB结果复制了已建立的PBE0/TZVP/CM5收费.
  • 开发了一个易于访问和与Mol* Viewer集成的Web应用程序.

主要成果:

  • PDBCharges能够快速计算PDB蛋白质结构的部分原子电荷.
  • 该应用程序以标准格式提供可下载的收费数据.
  • 使用Mol* Viewer进行交互式探索的集成可视化功能.

结论:

  • PDBCharges解决了对蛋白质部分原子电荷计算的准确和可访问工具的需求.
  • 该网络应用程序促进了蛋白质化学和结构生物学方面的研究.
  • 免费提供,不需要登录,PDBCharges促进广泛采用和使用.